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annotate macros.xml @ 0:26467f738ed4 draft

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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
author chemteam
date Tue, 12 Jul 2022 12:48:09 +0000
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26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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1 <macros>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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2 <token name="@TOOL_VERSION@">2022</token>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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3 <xml name="requirements">
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4 <requirements>
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5 <requirement type="package" version="@TOOL_VERSION@">gromacs</requirement>
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6 </requirements>
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7 </xml>
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8 <token name="@MAXWARN_CMD@">-maxwarn '$mxw'</token>
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9
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10 <xml name="citations">
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11 <citations>
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12 <citation type="doi">10.1016/j.softx.2015.06.001</citation>
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13 </citations>
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14 </xml>
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15 <xml name="md_inputs">
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16
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17 <conditional name="mdp">
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18 <param name="mdpfile" type="select" label="Parameter input">
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19 <option value="custom">Upload own MDP file</option>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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20 <option value="default">Use default (partially customisable) setting</option>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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21 </param>
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22 <when value="custom">
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23 <param argument="mdp_input" type="data" format='mdp' label="MD parameters (MDP) file (optional; default settings if not set)"/>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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24 </when>
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25 <when value="default">
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26 <param argument="integrator" type="select" label="Choice of integrator">
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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27 <option value="md">A leap-frog algorithm for integrating Newton's equations of motion.</option>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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28 <option value="sd">Stochastic dynamics integrator</option>
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29 <option value="bd">An Euler integrator for Brownian or position Langevin dynamics.</option>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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30 </param>
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31 <param argument="constraints" type="select" label="Bond constraints (constraints)">
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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32 <option value="none">No constraints except for those defined explicitly in the topology (none).</option>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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33 <option value="h-bonds">Bonds with H-atoms. (h-bonds).</option>
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34 <option value="all-bonds">All bonds (all-bonds).</option>
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35 <option value="h-angles">Bonds and angles with H-atoms. (h-angles).</option>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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36 <option value="all-angles">All bonds and angles (all-angles).</option>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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37 </param>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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38 <param argument="cutoffscheme" type="select" label="Neighbor searching">
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39 <option value="Verlet">Generate a pair list with buffering.</option>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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40 <option value="group">Generate a pair list for groups of atoms.</option>
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41 </param>
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42 <param argument="coulombtype" type="select" label="Electrostatics">
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43 <option value="PME">Fast smooth Particle-Mesh Ewald (SPME) electrostatics.</option>
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44 <option value="P3M-AD">Particle-Particle Particle-Mesh algorithm with analytical derivative.</option>
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45 <option value="Reaction-Field-zero">Reaction field electrostatics.</option>
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46 </param>
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47 <param name="temperature" type="integer" label="Temperature (K)" value="0" min="0" max="1000000" help="Temperature" />
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48 <param name="systemTcouple" type="select" label="Number of groups to set for thermocoupling">
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49 <option value="true">Single coupling group (System)</option>
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50 <option value="false" selected="true">Two coupling groups (Protein and Non-Protein)</option>
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51 </param>
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52 <param argument="step_length" type="float" label="Step length in ps" value="0" min="0.0001" max="1.0" help="Step length in ps." />
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53 <param argument="write_freq" type="integer" label="Number of steps that elapse between saving data points (velocities, forces, energies)" value="0" min="0" max="1000000" help="Step length in ps." />
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54 <param argument="rcoulomb" value="1.0" type="float" label="Distance for the Coulomb cut-off."/>
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55 <param argument="rlist" value="1.0" type="float" label="Cut-off distance for the short-range neighbor list. Ignored if the Verlet cutoff scheme is set."/>
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56 <param argument="rvdw" value="1.0" type="float" label="Short range van der Waals cutoff."/>
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57 <param argument="md_steps" type="integer" label="Number of steps for the simulation" value="0" min="0" help="MD steps" />
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58
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59 </when>
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61 </conditional>
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63 </xml>
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64
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65 <xml name="log">
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66 <param name="capture_log" type="boolean" value="false" label="Generate detailed log" help="Generate detailed log information that can be summarized with ParseLog."/>
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67 </xml>
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68
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69 <xml name="maxwarn">
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70 <param name="mxw" value="0" min="0" argument="-maxwarn" type="integer" label="Maximum warnings to allow." help="Do not use this unless you know what you are doing. This option allows you to override non-fatal warnings, that would otherwise cause the simulation to fail."/>
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71 </xml>
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74 <xml name="log_outputs">
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75 <data name="report" format="txt" from_work_dir="verbose.txt" label="GROMACS log file on ${on_string}">
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76 <filter>capture_log</filter>
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77 </data>
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78 </xml>
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79
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80 <xml name="xvg_or_tab">
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81 <param argument="fmt" type='select' label="Output format" help="Format for output; either standard GROMACS XVG, or Galaxy tabular file.">
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82 <option value="xvg">GROMACS XVG format</option>
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83 <option value="tabular" selected="true">Galaxy tabular</option>
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84 </param>
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85 </xml>
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86
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87 <xml name="xvg_or_tab_outputs" token_name="" token_label="">
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88 <data name="output1" format="xvg" from_work_dir="@NAME@.xvg" label="@LABEL@">
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89 <filter>fmt == 'xvg'</filter>
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90 </data>
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91 <data name="output2" format="tabular" from_work_dir="@NAME@.tabular" label="@LABEL@">
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92 <filter>fmt == 'tabular'</filter>
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93 </data>
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94 </xml>
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95
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96 <xml name="test_params">
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97 <param name="mdpfile" value="default" />
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98 <param name="step_length" value="0.002"/>
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99 <param name="md_steps" value="500"/>
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100 <param name="write_freq" value="50"/>
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101 <param name="temperature" value="300"/>
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102 <param name="integrator" value="md" />
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103 <param name="constraints" value="all-bonds"/>
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104 <param name="cutoffscheme" value="Verlet" />
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105 <param name="coulombtype" value="PME" />
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106 <param name="rlist" value="1.0" />
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107 <param name="rcoulomb" value="1.0" />
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108 <param name="rvdw" value="1.0" />
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109 </xml>
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110 </macros>